Criteria used in generating .dat files for LAMMPS in VOTCA

[Rishabh Guha]

Hey Christoph,

We had a quick question about csg_map. 

When we try to generate a cg data file from a lammps dump file using:-

csg_map --top topology.xml --trj xyz.dump --cg "xyz.xml;xyz.xml" --out xyz.gro

then what is the criteria on which these cg data files are generated? Is it a center of mass average? Is it the position of a certain atom in each molecule(like beta/alpha carbon) or some other criteria?

Regards

--

Rishabh Debraj Guha(PhD student)

Graduate Research Assistant

Mechanical and Aerospace Engineering

North Carolina State University

Contact:- +1-347-205-2280

[Christoph Junghans]

On Fri, Jul 30, 2021 at 10:24 AM Rishabh Guha <rdg...@ncsu.edu> wrote:
>
> Hey Christoph,
>
> We had a quick question about csg_map.
>
> When we try to generate a cg data file from a lammps dump file using:-
>
> csg_map --top topology.xml --trj xyz.dump --cg "xyz.xml;xyz.xml" --out xyz.gro
>
> then what is the criteria on which these cg data files are generated? Is it a center of mass average? Is it the position of a certain atom in each molecule(like beta/alpha carbon) or some other criteria?

Creating a mapping is art more than anything else. For polymers one
usually uses the center of mass mappings and turns every repeat unit
into a cg bead. But I have seens center of geometry or center of
charge before as well.

Christoph

>
> Regards
> --
> Rishabh Debraj Guha(PhD student)
>
> Graduate Research Assistant
> Mechanical and Aerospace Engineering
> North Carolina State University
> Contact:- +1-347-205-2280
>

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--
Christoph Junghans
Web: http://www.compphys.de